SAXSdb — 3icx

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Pre mRNA splicing protein

Sulfolobus solfataricus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q97ZH3_SULSO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–247； UniProt 135–380 Author chain B； PDBConstruct 2–247； UniProt 135–380 Author chain C； PDBConstruct 2–247； UniProt 135–380

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3icx
Deposition date deposition_date	2009-07-19
Structure title title	Crystal structure of Sulfolobus solfataricus Nop5 (135-380)
Keywords keywords	;C/D guide RNA, 2'-O-methylation, coiled-coil, RNA BINDING PROTEIN ;; RNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3icx__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3icx__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3icx__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	28.71 Å
Rg (electron density)	28.46 Å
Total Rg	29.06 Å
Atom count	3594
Residues	450
Excluded volume	64290 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3icx__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3icx__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3icxa_
Class class	a — All alpha proteins
Fold Fold fold	a.183 — Nop domain
Superfamily Superfamily superfamily	a.183.1 — Nop domain
Family Family family	a.183.1.0 — automated matches

Domain ID domain_id	d3icxb_
Class class	a — All alpha proteins
Fold Fold fold	a.183 — Nop domain
Superfamily Superfamily superfamily	a.183.1 — Nop domain
Family Family family	a.183.1.0 — automated matches

Domain ID domain_id	d3icxc_
Class class	a — All alpha proteins
Fold Fold fold	a.183 — Nop domain
Superfamily Superfamily superfamily	a.183.1 — Nop domain
Family Family family	a.183.1.0 — automated matches

CATH v4.4 (9 domains)

Domain ID domain_id	3icxA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	660 — Helix hairpin bin

Domain ID domain_id	3icxA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	460 —

Domain ID domain_id	3icxA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	90 — Nop domain

Domain ID domain_id	3icxB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	660 — Helix hairpin bin

Domain ID domain_id	3icxB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	460 —

Domain ID domain_id	3icxB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	90 — Nop domain

Domain ID domain_id	3icxC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	660 — Helix hairpin bin

Domain ID domain_id	3icxC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	460 —

Domain ID domain_id	3icxC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	90 — Nop domain

▶

Unit-cell length a length_a	153.645 Å
Unit-cell length b length_b	122.126 Å
Unit-cell length c length_c	71.786 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2630
R_work r_work	0.2610
R_free r_free	0.3040

Description description	Pre mRNA splicing protein
Molecular weight formula_weight	28890.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5386

Crystal structure of Sulfolobus solfataricus Nop5 (135-380)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Pre mRNA splicing protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3icx__assembly_2__model_1

3icx__assembly_2__model_1 | I(q)

3icx__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Source organism organism	Sulfolobus solfataricus
NCBI taxonomy ID ncbi_taxonomy_id	2287
Host organism host_organism	Escherichia coli

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Crystal structure of Sulfolobus solfataricus Nop5 (135-380)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Pre mRNA splicing protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3icx__assembly_2__model_1

3icx__assembly_2__model_1 | I(q)

3icx__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (1)